Hi Chris.
To get the coordinates of the nodes of a plotted tree (plotted with
plot.phylo or plotTree, among other functions), type:
plot(tree) ## for instance
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
The vectors obj$xx and obj$yy contain the coordinates of the nodes
(including the tips) of the tree in the order of the node indices of
tree$edge. So, for instance, should you know that you want to add an
element at the coordinates of the common ancestor of "t1" and "t8" you
could do:
anc<-fastMRCA(tree,"t1","t8") ## for example
points(obj$xx[anc],obj$yy[anc],pch=19)
This works for all different tree types in plot.phylo, plotTree, and
plot.simmap, and also for plotted phylomorphospaces (using
phytools::phylomorphospace), traitgrams (using phytools::phenogram), and
contMap or densityMap still graphs.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 5/11/2016 2:43 PM, Chris Buddenhagen wrote:
Is there a way to quickly associate a small graph created in R with
each node on a tree and have the graphic appear on the node when
plotted?
Or alternatively is there a way to get out the node coordinates of
each node for a given plot?
Sincerely
Chris Buddenhagen cbuddenha...@gmail.com
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